Table 1

Comparison of β-coefficients between conditional analyses in type 1 diabetes and LADA cohorts

SNP/HLA alleleLocusPositionAlleles (risk/other)WTCCC type 1 diabetes case vs. WTCCC control subjectsLADA case vs. control subjectsP
RAF, case subjectsRAF, control subjectsβSERAF, case subjectsRAF, control subjectsβSE
rs3957146HLA-DQA232789508T/C0.3850.1131.440.050.2510.1011.140.061.22 × 10−4
DQB1*0201HLA-DQB132739039P/A0.3380.1401.560.060.2090.1191.050.073.17 × 10−8
rs9268633HLA-DRA32514451G/A0.9830.8031.460.100.9190.8120.830.066.58 × 10−8
rs1610649HLA-G29876896G/A0.6160.5820.610.060.5920.5860.160.058.33 × 10−9
B*39HLA-B31431272P/A0.0430.0161.360.170.0230.0190.580.192.22 × 10−3
DRB1*0404HLA-DRB132660042P/A0.0820.0481.040.130.0370.0351.010.140.88
rs17427599HLA-DQB132775342T/C0.8490.7550.590.090.8180.7750.310.071.41 × 10−2
rs2301225HLA-DPA133143838T/C0.9410.8910.720.110.9240.8860.420.082.74 × 10−2
rs397081NOTCH432300595T/C0.0950.0450.790.120.0750.0540.640.100.34
rs9262545MUC2231101041A/G0.9130.8810.670.110.8620.8580.090.078.65 × 10−6
rs9262547MUC2231101206T/A0.1350.1191.590.190.1370.142−0.090.071.07 × 10−16
rs9259852HLA-A30004400C/T0.9770.9591.000.180.9680.9630.190.132.64 × 10−4
rs9269081HLA-DRA32549078A/C0.8900.7350.570.110.8210.6850.710.050.25
rs1978029HLA-DQB232839688C/T0.6510.5370.360.080.5650.4750.390.050.75
  • β-Coefficients and SEs are calculated for the risk allele frequency (RAF) from stepwise regression conditional on all SNP/HLA alleles (first column) in 1,985 type 1 diabetes case vs. 2,219 control subjects. β-Coefficients and SEs for LADA case vs. control subjects correspond with maximum effect size in conditional analysis. P values are derived from two-sample Z test to formally test whether β-coefficients are significantly different. Forest plot is shown in Supplementary Fig. 2. Three independent signals appeared in both type 1 diabetes and LADA conditional analyses (rs3957146, HLA-DRB1*0404, and rs9269081); however, of these three signals, only rs3957146 had a significant difference in effect size between type 1 diabetes and LADA (interaction P value = 4.15 × 10−10).